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Series GSE28286 Query DataSets for GSE28286
Status Public on Apr 04, 2011
Title Genome-wide analysis of transcription factor E2F1 mutant proteins reveals that N- and C-terminal protein interaction domains do not participate in targeting E2F1 to the human genome.
Project ENCODE
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Previous studies of E2F family members have suggested that protein-protein interactions may be the mechanism by which E2Fs are recruited to specific genomic regions. We have addressed this hypothesis on a genome-wide scale using ChIP-seq analysis of MCF7 cell lines that express tagged wildtype and mutant E2F1 proteins. First, we performed ChIP-seq for tagged wt E2F1. Then, we analyzed E2F1 proteins that lacked the N terminal SP1 and cyclin A binding domains, the C terminal transactivation and pocket protein binding domains, and the internal marked box domain. Surprisingly, we found that the ChIP-seq patterns of the mutant proteins were identical to that of wt E2F1. However, mutation of the DNA binding domain abrogated all E2F1 binding to the genome. These results suggested that the interaction between the E2F1 DNA binding domain and a consensus motif may be the primary determinant of E2F1 recruitment. To address this possibility, we analyzed the in vivo binding sites for the in vitro-derived consensus E2F1 motif (TTTSSCGC) and also performed de novo motif analysis. We found that only 12% of the ChIP-seq peaks contained the TTTSSCGC motif. De novo motif analysis indicated that most of the in vivo sites lacked the 5’ half of the in vitro derived consensus, having instead the in vivo consensus of CGCGC. In summary, our findings do not provide support for the model that protein-protein interactions are involved in recruiting E2F1 to the genome, but rather suggest that recognition of a motif found at most human promoters is the critical determinant.

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Overall design 9 total ChIP-seq datasets; four different HA-ER-E2F1 mutants, and one HA ER E2F1 wild type dataset done in duplicate, from 5 different stable cell lines derived from MCF7 cells; Three Input replicates from 2 different stable cell lines derived from MCF7 cells; HA ER E2F1 wild type duplicate dataset from MCF7 stable cells; 1 HA ER E2F1 DBDmut replicate from MCF7 stable cells cells, 1 HA ER E2F1ΔC replicate from MCF7 stable cells cells, 1 HA ER E2F1ΔN/C replicate from MCF7 stable cells cells, 1 HA ER E2F1ΔMB replicate from MCF7 stable cells cells, 1 HA ER E2F1ΔMB replicate from MCF7 stable cells cells, 3 Input replicates from MCF7 stable cells cells.
Web link
Contributor(s) Cao AR, Farnham PJ
Citation(s) 21310950
BioProject PRJNA63447
Submission date Mar 31, 2011
Last update date May 15, 2019
Contact name Philip Cayting
Organization name Stanford University
Department Genetics
Lab Snyder
Street address 1501 S California Ave
City Palo Alto
State/province CA
ZIP/Postal code 94304
Country USA
Platforms (1)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (9)
GSM699984 HA ER E2F1 wild type_MCF7 stables_ChIP-seq_rep1
GSM699985 HA ER E2F1 wild type_MCF7 stables_ChIP-seq_rep2
GSM699986 HA ER E2F1 DNA Binding Domain mutant_MCF7 stables_ChIP-seq_rep1
SRA SRP006205

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE28286_RAW.tar 1.9 Gb (http)(custom) TAR (of BAM)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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